A proposal to create a whale sanctuary in the southern Atlantic has been narrowly defeated at the annual meeting of the International Whaling Commission.

Argentina, Brazil, South Africa and Uruguay put forward a proposal to declare the southern Atlantic a no-kill zone for whales, a largely symbolic measure as no whaling currently takes place there.

Thirty-eight countries voted in favour and 21 voted against, with two abstentions - under the rules of the Commission, proposals need 75 per cent support for approval.

Mick McIntyre, director of the Pacific-based NGO Whales Alive, is at the IWC meeting in Panama City, and has told Radio Australia's Asia Pacific program it's regrettable several Pacific countries backed Japan, which led the opposition to the plan.

"What's regrettable is that these Pacific island countries do not have anything to do with whaling - so to support Japan in this way is out of character," he said.

"I can't comment on how well-versed these Pacific island countries are on this sanctuary proposal, but as I said, it's very much out of character for the conservation work that these Pacific island countries are trying to achieve.

"And we are working to convince these Pacific island countries, that it is of much more benefit to them, to support whale conservation, and to support whale eco-tourism, than to support Japanese whaling efforts."

Japan opposed the proposal, saying it lacked "scientific backing", and conservation groups have suggested aid commitments may have played a role in some countries joining the opposition.

But Shigehito Numata of the Japanese Fisheries Agency's whaling section says Tokyo's allies in the vote had made up their minds on the issues.

"We believe those nations cast votes from the perspective of sustainable use of marine resources," he said.

China, Russia and South Korea were also among those who voted against the proposal - and Mr McIntyre says he hopes that doesn't signal a shift in the way those countries think about whaling.

"Every species of whale that's ever been hunted has been done so to the brink of extinction," he said.

"It is not a fish stock, and I think that that's where a lot of countries get confused.

"This is a global animal that's highly-migratory, it doesn't belong to any one country and needs to be monitored by such a body as the International Whaling Commission."

Japan each year kills hundreds of whales in Antarctic waters that are already considered a sanctuary, as part of its scientific whaling program.